Former IB Special Director Rajinder Kumar, accused by CBI of murder in the Ishrat Jahan encounter case, was allegedly the brain behind the Home Ministry affidavit in which she was declared as a terrorist.

In its supplementary charge sheet in the encounter case, CBI has alleged that Kumar had given inputs to the Home Ministry that Ishrat was a terrorist to prove that the encounter in which the the 19-year-old victim Mumbai girl was killed along with three others was a genuine one, agency sources said.

The then Under Secretary in the Home Ministry, R V S Mani, gave two affidavits before the Gujarat High Court in less than two months, contradicting opinions on the antecedents of Ishrat, they said.

While the affidavit filed on August 6, 2009 stated that Ishrat and three others were terrorists, in the one filed on September 30, 2009, Mani claimed that there was no conclusive evidence to suggest she was a terrorist.

The agency has alleged that affidavit of August 6, 2009 was a brain child of Kumar who was allegedly apprehensive of his role coming under scrutiny in case a detailed probe is carried out in the encounter, which CBI has termed as fake.

Kumar said he did not want to react to the allegation but will reply to it at an appropriate forum.

“I will reply to them at an appropriate forum as and when it comes.

The process of generation of intelligence can never lead to any criminality. Neither me nor any team member have committed any criminal act by generating the intelligence,” Kumar said.

CBI sources said the supplementary charge sheet, which is also the concluding one in the case unless directed by the competent court, filed by the agency this week does not go into the antecedents of Ishrat.

“Nothing changes the fact that it was a joint counter terror operation of IB and Gujarat Police which was turned into a staged encounter. The antecedents of four victims does not change the fact that it was a fake encounter,” a senior CBI officer said.